The history of Zika virus disease serves as a paradigm of a typical emerging viral infection. Zika virus disease, a mosquito-borne flavivirus, was first isolated in 1947 in the Zika forest of Uganda. The same virus was also isolated from jungle-dwelling mosquitoes (Aedes [Stegomyia] africanus). In many areas of Africa and South Asia human infections with Zika virus were detected by both serology and virus isolation. About 80% of infections are asymptomatic, and in 20% a mostly mild disease with fever, rash, arthralgia, and conjunctivitis may occur. Fetal infections with malformations were not recorded in Africa or Asia. Zika virus was imported to northern Brazil possibly during the world soccer championship that was hosted by Brazil in June through July 2014. A cluster of severe fetal malformations with microcephaly and ocular defects was noted in 2015 in the northeast of Brazil, and intrauterine infections with Zika virus were confirmed. The dramatic change in Zika virus pathogenicity upon its introduction to Brazil has remained an enigma.

Microbiological risk analysis originated in the 1980s, with the publication of a seminal paper on dose-response assessment by Haas (23). Building on this, the first studies concerned the safety of drinking water. Viruses were important target organisms in these first studies. Most early risk assessments focused on enteroviruses and rotaviruses, for which culture methods and dose-response information were available (19, 20, 24, 37). These studies demonstrated that risks of viral contamination can be analyzed by the risk assessment paradigm. Risk assessments in the domain of food safety have focused primarily on bacterial pathogens, for which routine culture methods are generally available; quantitative information on the occurrence of bacteria along the food chain has been produced at an increasing pace. Methods to quantify infectious viruses (and protozoa) in foods are generally more complex or not available at all. This implies that quantitative risk assessment for these organisms is hampered by limited data availability even more than are risk assessments of bacterial pathogens.

This chapter focuses on the methodology used to detect animal viruses in samples of soil. This methodology generally relies on elution and subsequent concentration of viruses from the soil, after which either cytopathogenicity or plaque formation assays are used to detect the viruses. These assays are based on the use of cultured animal cells as hosts for viral replication. The chapter also describes the use of plaque formation methodology to detect bacteriophages, viruses which infect bacteria. Other types of assay procedures, such as those based on the PCR, have also been developed to detect viruses in soil samples. Many different types of apparatus can be used to collect soil samples. These range from spoons and spatulas to shovels and powered augers. The available options for suitable sample containers include wide-mouthed screw-cap plastic jars and zipper closure plastic bags. Soil samples should be kept chilled to reduce thermal inactivation of the viruses. Bacteriophages can be detected by direct assay of soil suspensions using a plaque formation technique. If the presence of soil particles in the assay causes a problem, either because the resulting turbidity obscures assessment of the results or the number of contaminating soil bacteria and fungi carried along with the soil particles complicates plaque enumeration, then the bacteriophages can be eluted from the soil particles and the eluate can be assayed.

Source Water Assessment and Protection Programs (SWAPPs) require states to delineate and assess the areas of land that contribute to public water systems using both surface and groundwaters. An integral part of these programs is an analysis of the susceptibilities of these systems to chemical and microbial contamination. There are several methods that can be used to establish placement of drinking water wells to minimize microbial contamination. The six most common delineation methods, listed in order of increasing technical complexity, are as follows: arbitrary-fixed-radius method; calculated-fixed-radius method; simplified variable shape method; analytical method; hydrogeologic mapping; and numerical transport models. An analysis of hydrogeology, an understanding of the contaminants and the factors that control their fate and transport in specific environments, and an analysis of the effectiveness of existing prevention and mitigation measures are essential so that states can apply the assessment results to source water protection. There are several components of the proposed groundwater rule (GWR) that require similar assessments of groundwater vulnerability or sensitivity to microbial contamination to those performed by the SWAPP. There are many different methods that can be used to delineate zones around drinking water wells to protect the water supply from microbial contamination. Finally, many of the wells that are used for drinking water are owned and operated by small communities and individual businesses.

This chapter provides a brief synopsis of the natural history of paralytic poliomyelitis, and gives an overview of the status of research concerning the molecular determinants of the pathogenesis of paralytic poliomyelitis. Determinants of the pathogenesis of poliomyelitis are either of viral origin, e.g., non-coding viral sequences, structural or nonstructural viral gene products, or of host origin, e.g., distribution of the cellular receptor and host cell factors required for viral replication. To provide a rational account of the relative contributions of a multitude of factors toward a complex phenomenon, the chapter is subdivided into sections dealing with the main parameters of poliovirus neurological disease. Tropism, neurovirulence, and conditions of the host are discussed separately. The chapter discusses experimental evidence for the genetic basis of neurovirulence in the 5’ non-translated region (5’ NTR) and the coding regions for the structural and nonstructural proteins of poliovirus. Extraneural determinants of neuropathogenicity, such as invasion of or spread within the CNS, combine with intraneural factors, such as IRES-mediated cell type specificity or the efficiency of genome replication. Excellent studies in nonhuman primates in the prevaccine era and recent progress through the advent of genetic engineering and transgenic animal models for human disease have afforded us detailed insight into the pathogenic mechanism of paralytic poliomyelitis.